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https://github.com/MillironX/nf-core_modules.git
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796dbb573e
* Remove old nextclade module * Add nextclade/datasetget and nextclade/run modules * Fix ECLint * Add reference and tag as inputs to datasetget module * Fix tests * Adjust spacing
42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
process NEXTCLADE_RUN {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/nextclade:1.9.0--h9ee0642_0' :
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'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }"
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input:
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tuple val(meta), path(fasta)
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path dataset
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output:
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tuple val(meta), path("${prefix}.csv") , emit: csv
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tuple val(meta), path("${prefix}.tsv") , emit: tsv
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tuple val(meta), path("${prefix}.json") , emit: json
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tuple val(meta), path("${prefix}.tree.json"), emit: json_tree
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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nextclade \\
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run \\
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$args \\
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--jobs $task.cpus \\
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--input-fasta $fasta \\
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--input-dataset $dataset \\
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--output-csv ${prefix}.csv \\
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--output-tsv ${prefix}.tsv \\
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--output-json ${prefix}.json \\
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--output-tree ${prefix}.tree.json \\
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--output-basename ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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nextclade: \$(nextclade --version 2>&1)
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END_VERSIONS
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"""
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}
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